Structural and mutational analyses of psychrophilic and mesophilic adenylate kinases highlight the role of hydrophobic interactions in protein thermal stability

Protein thermal stability is an important field since thermally stable proteins are desirable in many academic and industrial settings. Information on protein thermal stabilization can be obtained by comparing homologous proteins from organisms living at distinct temperatures. Here, we report structural and mutational analyses of adenylate kinases (AKs) from psychrophilic Bacillus globisporus (AKp) and mesophilic Bacillus subtilis (AKm). Sequence and structural comparison showed suboptimal hydrophobic packing around Thr26 in the CORE domain of AKp, which was replaced with an Ile residue in AKm. Mutations that improved hydrophobicity of the Thr residue increased the thermal stability of the psychrophilic AKp, and the largest stabilization was observed for a Thr-to-Ile substitution. Furthermore, a reverse Ile-to-Thr mutation in the mesophilic AKm significantly decreased thermal stability. We determined the crystal structures of mutant AKs to confirm the impact of the residue substitutions on the overall stability. Taken together, our results provide a structural basis for the stability difference between psychrophilic and mesophilic AK homologues and highlight the role of hydrophobic interactions in protein thermal stability

Prediction of EOS and Elastic modulus of Ni/Al nanopowder and nanofoil by Molecular Dynamics

There are numerous studies regarding Ni/Al alloy for its extreme reactivity, which can be used for various applications, but not in the forms of nanopowder and nanofoil. Thus, we have obtained the equation of state and elastic modulus of Ni/Al alloy in those structures. We have made various model systems to check the equation of state of each material (i.e. Ni and Al) and elastic modulus at different conditions (e.g. stoichiometric ratio and nanocluster size for ???nanopowder???, layer thickness and layer frequency for ???nanofoil??? at different temperature and pressure). We employed classical Molecular Dynamics (MD) with Modified Embedded-Atom Method (MEAM) Potential, of which parameters are based on thermal and mechanical properties. Furthermore, through Coarse-Grained Molecular Dynamics (CGMD), the behavior of phase changes of those structures was investigated in terms of size

Patient-specific, deliverable, and self-expandable surgical guide development and evaluation using 4D printing for laparoscopic partial nephrectomy

Abstract Accurate lesion diagnosis through computed tomography (CT) and advances in laparoscopic or robotic surgeries have increased partial nephrectomy survival rates. However, accurately marking the kidney resection area through the laparoscope is a prevalent challenge. Therefore, we fabricated and evaluated a 4D-printed kidney surgical guide (4DP-KSG) for laparoscopic partial nephrectomies based on CT images. The kidney phantom and 4DP-KSG were designed based on CT images from a renal cell carcinoma patient. 4DP-KSG were fabricated using shape-memory polymers. 4DP-KSG was compressed to a 10 mm thickness and restored to simulate laparoscopic port passage. The Bland–Altman evaluation assessed 4DP-KSG shape and marking accuracies before compression and after restoration with three operators. The kidney phantom’s shape accuracy was 0.436 ± 0.333 mm, and the 4DP-KSG’s shape accuracy was 0.818 ± 0.564 mm before compression and 0.389 ± 0.243 mm after restoration, with no significant differences. The 4DP-KSG marking accuracy was 0.952 ± 0.682 mm before compression and 0.793 ± 0.677 mm after restoration, with no statistical differences between operators (p = 0.899 and 0.992). In conclusion, our 4DP-KSG can be used for laparoscopic partial nephrectomies, providing precise and quantitative kidney tumor marking between operators before compression and after restoration

Conformational dynamics of adenylate kinase in crystals

Adenylate kinase is a ubiquitous enzyme in living systems and undergoes dramatic conformational changes during its catalytic cycle. For these reasons, it is widely studied by genetic, biochemical, and biophysical methods, both experimental and theoretical. We have determined the basic crystal structures of three differently liganded states of adenylate kinase from Methanotorrus igneus, a hyperthermophilic organism whose adenylate kinase is a homotrimeric oligomer. The multiple copies of each protomer in the asymmetric unit of the crystal provide a unique opportunity to study the variation in the structure and were further analyzed using advanced crystallographic refinement methods and analysis tools to reveal conformational heterogeneity and, thus, implied dynamic behaviors in the catalytic cycle

Ulvophyte Green Algae Caulerpa lentillifera: Metabolites Profile and Antioxidant, Anticancer, Anti-Obesity, and In Vitro Cytotoxicity Properties

Marine algae have excellent bioresource properties with potential nutritional and bioactive therapeutic benefits, but studies regarding Caulerpa lentillifera are limited. This study aims to explore the metabolites profile and the antioxidant, anticancer, anti-obesity, and in vitro cytotoxicity properties of fractionated ethanolic extract of C. lentillifera using two maceration and soxhlet extraction methods. Dried simplicia of C. lentillifera was mashed and extracted in ethanol solvent, concentrated and evaporated, then sequentially partitioned with equal volumes of ethyl acetate and n-Hexane. Six samples were used in this study, consisting of ME (Maceration—Ethanol), MEA (Maceration—Ethyl Acetate), MH (Maceration—n-Hexane), SE (Soxhletation—Ethanol), SEA (Soxhletation—Ethyl Acetate), and SH (Soxhletation—n-Hexane). Non-targeted metabolomic profiling was determined using LC-HRMS, while antioxidant, anti-obesity, and anticancer cytotoxicity were determined using DPPH and ABTS, lipase inhibition, and MTT assay, respectively. This study demonstrates that C. lentillifera has several functional metabolites, antioxidant capacity (EC50 MH is very close to EC50 of Trolox), as well as anti-obesity properties (EC50 MH < EC50 orlistat, an inhibitor of lipid hydrolyzing enzymes), which are useful as precursors for new therapeutic approaches in improving obesity-related diseases. More interestingly, ME, MH, and SE are novel bioresource agents for anticancer drugs, especially for hepatoma, breast, colorectal, and leukemia cancers. Finally, C. lentillifera can be a nutraceutical with great therapeutic benefits

Ulvophyte Green Algae <i>Caulerpa lentillifera</i>: Metabolites Profile and Antioxidant, Anticancer, Anti-Obesity, and In Vitro Cytotoxicity Properties

Marine algae have excellent bioresource properties with potential nutritional and bioactive therapeutic benefits, but studies regarding Caulerpa lentillifera are limited. This study aims to explore the metabolites profile and the antioxidant, anticancer, anti-obesity, and in vitro cytotoxicity properties of fractionated ethanolic extract of C. lentillifera using two maceration and soxhlet extraction methods. Dried simplicia of C. lentillifera was mashed and extracted in ethanol solvent, concentrated and evaporated, then sequentially partitioned with equal volumes of ethyl acetate and n-Hexane. Six samples were used in this study, consisting of ME (Maceration—Ethanol), MEA (Maceration—Ethyl Acetate), MH (Maceration—n-Hexane), SE (Soxhletation—Ethanol), SEA (Soxhletation—Ethyl Acetate), and SH (Soxhletation—n-Hexane). Non-targeted metabolomic profiling was determined using LC-HRMS, while antioxidant, anti-obesity, and anticancer cytotoxicity were determined using DPPH and ABTS, lipase inhibition, and MTT assay, respectively. This study demonstrates that C. lentillifera has several functional metabolites, antioxidant capacity (EC50 MH is very close to EC50 of Trolox), as well as anti-obesity properties (EC50 MH 50 orlistat, an inhibitor of lipid hydrolyzing enzymes), which are useful as precursors for new therapeutic approaches in improving obesity-related diseases. More interestingly, ME, MH, and SE are novel bioresource agents for anticancer drugs, especially for hepatoma, breast, colorectal, and leukemia cancers. Finally, C. lentillifera can be a nutraceutical with great therapeutic benefits